1 Data preparation

1.1 Outline

  • Load scripts: loads libraries and useful scripts used in the analyses; all .R files contained in scripts at the root of the factory are automatically loaded

  • Load data: imports datasets, and may contain some ad hoc changes to the data such as specific data cleaning (not used in other reports), new variables used in the analyses, etc.

1.2 Load packages


library(reportfactory)
library(here)
library(rio) 
library(tidyverse)
library(incidence)
library(distcrete)
library(epitrix)
library(earlyR)
library(projections)
library(linelist)
library(remotes)
library(janitor)
library(kableExtra)
library(DT)
library(cyphr)
library(chngpt)
library(lubridate)
library(ggpubr)
library(ggnewscale)

1.3 Load scripts

These scripts will load:

  • all scripts stored as .R files inside /scripts/
  • all scripts stored as .R files inside /src/

These scripts also contain routines to access the latest clean encrypted data (see next section).


reportfactory::rfh_load_scripts()

1.4 Load clean data

We import the latest NHS pathways data:


x <- import_pathways() %>%
  as_tibble()
x
## # A tibble: 171,895 x 11
##    site_type date       sex   age   ccg_code ccg_name count postcode nhs_region
##    <chr>     <date>     <chr> <chr> <chr>    <chr>    <int> <chr>    <chr>     
##  1 111       2020-03-18 fema… miss… e380000… nhs_glo…     1 gl34fe   South West
##  2 111       2020-03-18 fema… miss… e380001… nhs_sou…     1 ne325nn  North Eas…
##  3 111       2020-03-18 fema… 0-18  e380000… nhs_air…     8 bd57jr   North Eas…
##  4 111       2020-03-18 fema… 0-18  e380000… nhs_ash…     7 tn254ab  South East
##  5 111       2020-03-18 fema… 0-18  e380000… nhs_bar…    35 rm13ae   London    
##  6 111       2020-03-18 fema… 0-18  e380000… nhs_bar…     9 n111np   London    
##  7 111       2020-03-18 fema… 0-18  e380000… nhs_bar…    11 s752py   North Eas…
##  8 111       2020-03-18 fema… 0-18  e380000… nhs_bas…    19 ss143hg  East of E…
##  9 111       2020-03-18 fema… 0-18  e380000… nhs_bas…     6 dn227xf  North Eas…
## 10 111       2020-03-18 fema… 0-18  e380000… nhs_bat…     9 ba25rp   South West
## # … with 171,885 more rows, and 2 more variables: day <int>, weekday <fct>

We also import demographics data for NHS regions in England, used later in our analysis:


path <- here::here("data", "csv", "nhs_region_population_2018.csv")
nhs_region_pop <- rio::import(path) %>%
  mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))

nhs_region_pop$nhs_region <- gsub(" Of ", " of ", nhs_region_pop$nhs_region)
nhs_region_pop$nhs_region <- gsub(" And ", " and ", nhs_region_pop$nhs_region)
nhs_region_pop
##                  nhs_region variable      value
## 1                North West     0-18 0.22538599
## 2  North East and Yorkshire     0-18 0.21876449
## 3                  Midlands     0-18 0.22564656
## 4           East of England     0-18 0.22810783
## 5                    London     0-18 0.23764782
## 6                South East     0-18 0.22458811
## 7                South West     0-18 0.20799797
## 8                North West    19-69 0.64274078
## 9  North East and Yorkshire    19-69 0.64437753
## 10                 Midlands    19-69 0.63876675
## 11          East of England    19-69 0.63034229
## 12                   London    19-69 0.67820084
## 13               South East    19-69 0.63267336
## 14               South West    19-69 0.63176131
## 15               North West   70-120 0.13187323
## 16 North East and Yorkshire   70-120 0.13685797
## 17                 Midlands   70-120 0.13558669
## 18          East of England   70-120 0.14154988
## 19                   London   70-120 0.08415135
## 20               South East   70-120 0.14273853
## 21               South West   70-120 0.16024072

Finally, we import publically available deaths per NHS region:


dth <- import_deaths() %>%
  mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))

#truncation to account for reporting delay
delay_max <- 21

dth$nhs_region <- gsub(" Of ", " of ", dth$nhs_region)
dth$nhs_region <- gsub(" And ", " and ", dth$nhs_region)
dth
##     date_report               nhs_region deaths
## 1    2020-03-01          East of England      0
## 2    2020-03-02          East of England      1
## 3    2020-03-03          East of England      0
## 4    2020-03-04          East of England      0
## 5    2020-03-05          East of England      0
## 6    2020-03-06          East of England      1
## 7    2020-03-07          East of England      0
## 8    2020-03-08          East of England      0
## 9    2020-03-09          East of England      1
## 10   2020-03-10          East of England      0
## 11   2020-03-11          East of England      0
## 12   2020-03-12          East of England      0
## 13   2020-03-13          East of England      1
## 14   2020-03-14          East of England      2
## 15   2020-03-15          East of England      2
## 16   2020-03-16          East of England      1
## 17   2020-03-17          East of England      1
## 18   2020-03-18          East of England      5
## 19   2020-03-19          East of England      4
## 20   2020-03-20          East of England      2
## 21   2020-03-21          East of England     11
## 22   2020-03-22          East of England     12
## 23   2020-03-23          East of England     11
## 24   2020-03-24          East of England     19
## 25   2020-03-25          East of England     26
## 26   2020-03-26          East of England     36
## 27   2020-03-27          East of England     38
## 28   2020-03-28          East of England     28
## 29   2020-03-29          East of England     43
## 30   2020-03-30          East of England     45
## 31   2020-03-31          East of England     70
## 32   2020-04-01          East of England     62
## 33   2020-04-02          East of England     65
## 34   2020-04-03          East of England     80
## 35   2020-04-04          East of England     71
## 36   2020-04-05          East of England     76
## 37   2020-04-06          East of England     71
## 38   2020-04-07          East of England     93
## 39   2020-04-08          East of England    111
## 40   2020-04-09          East of England     87
## 41   2020-04-10          East of England     74
## 42   2020-04-11          East of England     92
## 43   2020-04-12          East of England    100
## 44   2020-04-13          East of England     78
## 45   2020-04-14          East of England     61
## 46   2020-04-15          East of England     82
## 47   2020-04-16          East of England     74
## 48   2020-04-17          East of England     86
## 49   2020-04-18          East of England     64
## 50   2020-04-19          East of England     67
## 51   2020-04-20          East of England     67
## 52   2020-04-21          East of England     75
## 53   2020-04-22          East of England     67
## 54   2020-04-23          East of England     49
## 55   2020-04-24          East of England     66
## 56   2020-04-25          East of England     54
## 57   2020-04-26          East of England     48
## 58   2020-04-27          East of England     46
## 59   2020-04-28          East of England     58
## 60   2020-04-29          East of England     32
## 61   2020-04-30          East of England     45
## 62   2020-05-01          East of England     49
## 63   2020-05-02          East of England     29
## 64   2020-05-03          East of England     41
## 65   2020-05-04          East of England     19
## 66   2020-05-05          East of England     36
## 67   2020-05-06          East of England     31
## 68   2020-05-07          East of England     33
## 69   2020-05-08          East of England     33
## 70   2020-05-09          East of England     29
## 71   2020-05-10          East of England     22
## 72   2020-05-11          East of England     18
## 73   2020-05-12          East of England     21
## 74   2020-05-13          East of England     27
## 75   2020-05-14          East of England     26
## 76   2020-05-15          East of England     19
## 77   2020-05-16          East of England     26
## 78   2020-05-17          East of England     17
## 79   2020-05-18          East of England     25
## 80   2020-05-19          East of England     15
## 81   2020-05-20          East of England     26
## 82   2020-05-21          East of England     21
## 83   2020-05-22          East of England     13
## 84   2020-05-23          East of England     12
## 85   2020-05-24          East of England     17
## 86   2020-05-25          East of England     25
## 87   2020-05-26          East of England     14
## 88   2020-05-27          East of England     12
## 89   2020-05-28          East of England     17
## 90   2020-05-29          East of England     16
## 91   2020-05-30          East of England      9
## 92   2020-05-31          East of England      8
## 93   2020-06-01          East of England     17
## 94   2020-06-02          East of England     14
## 95   2020-06-03          East of England     10
## 96   2020-06-04          East of England      7
## 97   2020-06-05          East of England     14
## 98   2020-06-06          East of England      5
## 99   2020-06-07          East of England      9
## 100  2020-06-08          East of England      7
## 101  2020-06-09          East of England      6
## 102  2020-06-10          East of England      8
## 103  2020-06-11          East of England      1
## 104  2020-06-12          East of England      9
## 105  2020-06-13          East of England      5
## 106  2020-06-14          East of England      4
## 107  2020-06-15          East of England      8
## 108  2020-06-16          East of England      3
## 109  2020-06-17          East of England      7
## 110  2020-06-18          East of England      4
## 111  2020-06-19          East of England      7
## 112  2020-06-20          East of England      4
## 113  2020-06-21          East of England      3
## 114  2020-06-22          East of England      6
## 115  2020-06-23          East of England      5
## 116  2020-06-24          East of England      4
## 117  2020-06-25          East of England      1
## 118  2020-06-26          East of England      5
## 119  2020-06-27          East of England      6
## 120  2020-06-28          East of England      8
## 121  2020-06-29          East of England      4
## 122  2020-06-30          East of England      5
## 123  2020-07-01          East of England      2
## 124  2020-07-02          East of England      5
## 125  2020-07-03          East of England      0
## 126  2020-07-04          East of England      3
## 127  2020-07-05          East of England      1
## 128  2020-07-06          East of England      2
## 129  2020-07-07          East of England      1
## 130  2020-07-08          East of England      0
## 131  2020-07-09          East of England      5
## 132  2020-07-10          East of England      0
## 133  2020-03-01                   London      0
## 134  2020-03-02                   London      0
## 135  2020-03-03                   London      0
## 136  2020-03-04                   London      0
## 137  2020-03-05                   London      0
## 138  2020-03-06                   London      1
## 139  2020-03-07                   London      0
## 140  2020-03-08                   London      0
## 141  2020-03-09                   London      1
## 142  2020-03-10                   London      0
## 143  2020-03-11                   London      5
## 144  2020-03-12                   London      6
## 145  2020-03-13                   London     10
## 146  2020-03-14                   London     13
## 147  2020-03-15                   London      9
## 148  2020-03-16                   London     15
## 149  2020-03-17                   London     23
## 150  2020-03-18                   London     27
## 151  2020-03-19                   London     25
## 152  2020-03-20                   London     44
## 153  2020-03-21                   London     49
## 154  2020-03-22                   London     54
## 155  2020-03-23                   London     63
## 156  2020-03-24                   London     86
## 157  2020-03-25                   London    112
## 158  2020-03-26                   London    129
## 159  2020-03-27                   London    129
## 160  2020-03-28                   London    122
## 161  2020-03-29                   London    145
## 162  2020-03-30                   London    149
## 163  2020-03-31                   London    181
## 164  2020-04-01                   London    202
## 165  2020-04-02                   London    191
## 166  2020-04-03                   London    196
## 167  2020-04-04                   London    230
## 168  2020-04-05                   London    195
## 169  2020-04-06                   London    197
## 170  2020-04-07                   London    220
## 171  2020-04-08                   London    238
## 172  2020-04-09                   London    206
## 173  2020-04-10                   London    170
## 174  2020-04-11                   London    178
## 175  2020-04-12                   London    158
## 176  2020-04-13                   London    166
## 177  2020-04-14                   London    143
## 178  2020-04-15                   London    142
## 179  2020-04-16                   London    140
## 180  2020-04-17                   London    100
## 181  2020-04-18                   London    101
## 182  2020-04-19                   London    103
## 183  2020-04-20                   London     95
## 184  2020-04-21                   London     94
## 185  2020-04-22                   London    109
## 186  2020-04-23                   London     77
## 187  2020-04-24                   London     71
## 188  2020-04-25                   London     58
## 189  2020-04-26                   London     53
## 190  2020-04-27                   London     51
## 191  2020-04-28                   London     44
## 192  2020-04-29                   London     45
## 193  2020-04-30                   London     40
## 194  2020-05-01                   London     41
## 195  2020-05-02                   London     41
## 196  2020-05-03                   London     36
## 197  2020-05-04                   London     30
## 198  2020-05-05                   London     25
## 199  2020-05-06                   London     37
## 200  2020-05-07                   London     37
## 201  2020-05-08                   London     30
## 202  2020-05-09                   London     23
## 203  2020-05-10                   London     26
## 204  2020-05-11                   London     18
## 205  2020-05-12                   London     18
## 206  2020-05-13                   London     17
## 207  2020-05-14                   London     20
## 208  2020-05-15                   London     18
## 209  2020-05-16                   London     14
## 210  2020-05-17                   London     15
## 211  2020-05-18                   London     10
## 212  2020-05-19                   London     14
## 213  2020-05-20                   London     19
## 214  2020-05-21                   London     12
## 215  2020-05-22                   London     10
## 216  2020-05-23                   London      6
## 217  2020-05-24                   London      7
## 218  2020-05-25                   London      9
## 219  2020-05-26                   London     13
## 220  2020-05-27                   London      7
## 221  2020-05-28                   London      8
## 222  2020-05-29                   London      7
## 223  2020-05-30                   London     12
## 224  2020-05-31                   London      6
## 225  2020-06-01                   London     10
## 226  2020-06-02                   London      8
## 227  2020-06-03                   London      6
## 228  2020-06-04                   London      8
## 229  2020-06-05                   London      4
## 230  2020-06-06                   London      0
## 231  2020-06-07                   London      5
## 232  2020-06-08                   London      5
## 233  2020-06-09                   London      4
## 234  2020-06-10                   London      7
## 235  2020-06-11                   London      5
## 236  2020-06-12                   London      3
## 237  2020-06-13                   London      3
## 238  2020-06-14                   London      3
## 239  2020-06-15                   London      1
## 240  2020-06-16                   London      2
## 241  2020-06-17                   London      1
## 242  2020-06-18                   London      2
## 243  2020-06-19                   London      5
## 244  2020-06-20                   London      3
## 245  2020-06-21                   London      4
## 246  2020-06-22                   London      2
## 247  2020-06-23                   London      1
## 248  2020-06-24                   London      4
## 249  2020-06-25                   London      3
## 250  2020-06-26                   London      2
## 251  2020-06-27                   London      1
## 252  2020-06-28                   London      2
## 253  2020-06-29                   London      2
## 254  2020-06-30                   London      1
## 255  2020-07-01                   London      2
## 256  2020-07-02                   London      2
## 257  2020-07-03                   London      2
## 258  2020-07-04                   London      1
## 259  2020-07-05                   London      3
## 260  2020-07-06                   London      2
## 261  2020-07-07                   London      1
## 262  2020-07-08                   London      3
## 263  2020-07-09                   London      0
## 264  2020-07-10                   London      0
## 265  2020-03-01                 Midlands      0
## 266  2020-03-02                 Midlands      0
## 267  2020-03-03                 Midlands      1
## 268  2020-03-04                 Midlands      0
## 269  2020-03-05                 Midlands      0
## 270  2020-03-06                 Midlands      0
## 271  2020-03-07                 Midlands      0
## 272  2020-03-08                 Midlands      2
## 273  2020-03-09                 Midlands      1
## 274  2020-03-10                 Midlands      0
## 275  2020-03-11                 Midlands      2
## 276  2020-03-12                 Midlands      6
## 277  2020-03-13                 Midlands      5
## 278  2020-03-14                 Midlands      4
## 279  2020-03-15                 Midlands      5
## 280  2020-03-16                 Midlands     11
## 281  2020-03-17                 Midlands      8
## 282  2020-03-18                 Midlands     13
## 283  2020-03-19                 Midlands      8
## 284  2020-03-20                 Midlands     28
## 285  2020-03-21                 Midlands     13
## 286  2020-03-22                 Midlands     31
## 287  2020-03-23                 Midlands     33
## 288  2020-03-24                 Midlands     41
## 289  2020-03-25                 Midlands     48
## 290  2020-03-26                 Midlands     64
## 291  2020-03-27                 Midlands     72
## 292  2020-03-28                 Midlands     89
## 293  2020-03-29                 Midlands     92
## 294  2020-03-30                 Midlands     90
## 295  2020-03-31                 Midlands    123
## 296  2020-04-01                 Midlands    140
## 297  2020-04-02                 Midlands    142
## 298  2020-04-03                 Midlands    124
## 299  2020-04-04                 Midlands    151
## 300  2020-04-05                 Midlands    164
## 301  2020-04-06                 Midlands    140
## 302  2020-04-07                 Midlands    123
## 303  2020-04-08                 Midlands    186
## 304  2020-04-09                 Midlands    139
## 305  2020-04-10                 Midlands    127
## 306  2020-04-11                 Midlands    142
## 307  2020-04-12                 Midlands    139
## 308  2020-04-13                 Midlands    120
## 309  2020-04-14                 Midlands    116
## 310  2020-04-15                 Midlands    147
## 311  2020-04-16                 Midlands    102
## 312  2020-04-17                 Midlands    118
## 313  2020-04-18                 Midlands    115
## 314  2020-04-19                 Midlands     92
## 315  2020-04-20                 Midlands    107
## 316  2020-04-21                 Midlands     86
## 317  2020-04-22                 Midlands     78
## 318  2020-04-23                 Midlands    103
## 319  2020-04-24                 Midlands     79
## 320  2020-04-25                 Midlands     72
## 321  2020-04-26                 Midlands     81
## 322  2020-04-27                 Midlands     74
## 323  2020-04-28                 Midlands     68
## 324  2020-04-29                 Midlands     53
## 325  2020-04-30                 Midlands     56
## 326  2020-05-01                 Midlands     64
## 327  2020-05-02                 Midlands     51
## 328  2020-05-03                 Midlands     52
## 329  2020-05-04                 Midlands     61
## 330  2020-05-05                 Midlands     59
## 331  2020-05-06                 Midlands     59
## 332  2020-05-07                 Midlands     48
## 333  2020-05-08                 Midlands     34
## 334  2020-05-09                 Midlands     37
## 335  2020-05-10                 Midlands     42
## 336  2020-05-11                 Midlands     33
## 337  2020-05-12                 Midlands     45
## 338  2020-05-13                 Midlands     40
## 339  2020-05-14                 Midlands     37
## 340  2020-05-15                 Midlands     40
## 341  2020-05-16                 Midlands     34
## 342  2020-05-17                 Midlands     31
## 343  2020-05-18                 Midlands     35
## 344  2020-05-19                 Midlands     34
## 345  2020-05-20                 Midlands     36
## 346  2020-05-21                 Midlands     32
## 347  2020-05-22                 Midlands     27
## 348  2020-05-23                 Midlands     34
## 349  2020-05-24                 Midlands     20
## 350  2020-05-25                 Midlands     26
## 351  2020-05-26                 Midlands     33
## 352  2020-05-27                 Midlands     29
## 353  2020-05-28                 Midlands     28
## 354  2020-05-29                 Midlands     20
## 355  2020-05-30                 Midlands     21
## 356  2020-05-31                 Midlands     22
## 357  2020-06-01                 Midlands     20
## 358  2020-06-02                 Midlands     22
## 359  2020-06-03                 Midlands     24
## 360  2020-06-04                 Midlands     16
## 361  2020-06-05                 Midlands     21
## 362  2020-06-06                 Midlands     20
## 363  2020-06-07                 Midlands     17
## 364  2020-06-08                 Midlands     16
## 365  2020-06-09                 Midlands     18
## 366  2020-06-10                 Midlands     15
## 367  2020-06-11                 Midlands     13
## 368  2020-06-12                 Midlands     12
## 369  2020-06-13                 Midlands      6
## 370  2020-06-14                 Midlands     18
## 371  2020-06-15                 Midlands     12
## 372  2020-06-16                 Midlands     15
## 373  2020-06-17                 Midlands     11
## 374  2020-06-18                 Midlands     15
## 375  2020-06-19                 Midlands     10
## 376  2020-06-20                 Midlands     15
## 377  2020-06-21                 Midlands     13
## 378  2020-06-22                 Midlands     14
## 379  2020-06-23                 Midlands     16
## 380  2020-06-24                 Midlands     15
## 381  2020-06-25                 Midlands     18
## 382  2020-06-26                 Midlands      5
## 383  2020-06-27                 Midlands      5
## 384  2020-06-28                 Midlands      7
## 385  2020-06-29                 Midlands      6
## 386  2020-06-30                 Midlands      6
## 387  2020-07-01                 Midlands      7
## 388  2020-07-02                 Midlands      9
## 389  2020-07-03                 Midlands      3
## 390  2020-07-04                 Midlands      4
## 391  2020-07-05                 Midlands      6
## 392  2020-07-06                 Midlands      5
## 393  2020-07-07                 Midlands      3
## 394  2020-07-08                 Midlands      5
## 395  2020-07-09                 Midlands      6
## 396  2020-07-10                 Midlands      0
## 397  2020-03-01 North East and Yorkshire      0
## 398  2020-03-02 North East and Yorkshire      0
## 399  2020-03-03 North East and Yorkshire      0
## 400  2020-03-04 North East and Yorkshire      0
## 401  2020-03-05 North East and Yorkshire      0
## 402  2020-03-06 North East and Yorkshire      0
## 403  2020-03-07 North East and Yorkshire      0
## 404  2020-03-08 North East and Yorkshire      0
## 405  2020-03-09 North East and Yorkshire      0
## 406  2020-03-10 North East and Yorkshire      0
## 407  2020-03-11 North East and Yorkshire      0
## 408  2020-03-12 North East and Yorkshire      0
## 409  2020-03-13 North East and Yorkshire      0
## 410  2020-03-14 North East and Yorkshire      0
## 411  2020-03-15 North East and Yorkshire      2
## 412  2020-03-16 North East and Yorkshire      3
## 413  2020-03-17 North East and Yorkshire      1
## 414  2020-03-18 North East and Yorkshire      2
## 415  2020-03-19 North East and Yorkshire      6
## 416  2020-03-20 North East and Yorkshire      5
## 417  2020-03-21 North East and Yorkshire      6
## 418  2020-03-22 North East and Yorkshire      7
## 419  2020-03-23 North East and Yorkshire      9
## 420  2020-03-24 North East and Yorkshire      8
## 421  2020-03-25 North East and Yorkshire     18
## 422  2020-03-26 North East and Yorkshire     21
## 423  2020-03-27 North East and Yorkshire     28
## 424  2020-03-28 North East and Yorkshire     35
## 425  2020-03-29 North East and Yorkshire     38
## 426  2020-03-30 North East and Yorkshire     64
## 427  2020-03-31 North East and Yorkshire     60
## 428  2020-04-01 North East and Yorkshire     67
## 429  2020-04-02 North East and Yorkshire     75
## 430  2020-04-03 North East and Yorkshire    100
## 431  2020-04-04 North East and Yorkshire    105
## 432  2020-04-05 North East and Yorkshire     92
## 433  2020-04-06 North East and Yorkshire     96
## 434  2020-04-07 North East and Yorkshire    102
## 435  2020-04-08 North East and Yorkshire    107
## 436  2020-04-09 North East and Yorkshire    111
## 437  2020-04-10 North East and Yorkshire    117
## 438  2020-04-11 North East and Yorkshire     98
## 439  2020-04-12 North East and Yorkshire     84
## 440  2020-04-13 North East and Yorkshire     94
## 441  2020-04-14 North East and Yorkshire    107
## 442  2020-04-15 North East and Yorkshire     96
## 443  2020-04-16 North East and Yorkshire    103
## 444  2020-04-17 North East and Yorkshire     88
## 445  2020-04-18 North East and Yorkshire     95
## 446  2020-04-19 North East and Yorkshire     88
## 447  2020-04-20 North East and Yorkshire    100
## 448  2020-04-21 North East and Yorkshire     76
## 449  2020-04-22 North East and Yorkshire     84
## 450  2020-04-23 North East and Yorkshire     63
## 451  2020-04-24 North East and Yorkshire     72
## 452  2020-04-25 North East and Yorkshire     69
## 453  2020-04-26 North East and Yorkshire     65
## 454  2020-04-27 North East and Yorkshire     65
## 455  2020-04-28 North East and Yorkshire     57
## 456  2020-04-29 North East and Yorkshire     69
## 457  2020-04-30 North East and Yorkshire     57
## 458  2020-05-01 North East and Yorkshire     64
## 459  2020-05-02 North East and Yorkshire     48
## 460  2020-05-03 North East and Yorkshire     40
## 461  2020-05-04 North East and Yorkshire     49
## 462  2020-05-05 North East and Yorkshire     40
## 463  2020-05-06 North East and Yorkshire     51
## 464  2020-05-07 North East and Yorkshire     45
## 465  2020-05-08 North East and Yorkshire     42
## 466  2020-05-09 North East and Yorkshire     44
## 467  2020-05-10 North East and Yorkshire     40
## 468  2020-05-11 North East and Yorkshire     29
## 469  2020-05-12 North East and Yorkshire     27
## 470  2020-05-13 North East and Yorkshire     28
## 471  2020-05-14 North East and Yorkshire     31
## 472  2020-05-15 North East and Yorkshire     32
## 473  2020-05-16 North East and Yorkshire     35
## 474  2020-05-17 North East and Yorkshire     26
## 475  2020-05-18 North East and Yorkshire     30
## 476  2020-05-19 North East and Yorkshire     27
## 477  2020-05-20 North East and Yorkshire     22
## 478  2020-05-21 North East and Yorkshire     33
## 479  2020-05-22 North East and Yorkshire     22
## 480  2020-05-23 North East and Yorkshire     18
## 481  2020-05-24 North East and Yorkshire     26
## 482  2020-05-25 North East and Yorkshire     21
## 483  2020-05-26 North East and Yorkshire     21
## 484  2020-05-27 North East and Yorkshire     22
## 485  2020-05-28 North East and Yorkshire     21
## 486  2020-05-29 North East and Yorkshire     25
## 487  2020-05-30 North East and Yorkshire     20
## 488  2020-05-31 North East and Yorkshire     20
## 489  2020-06-01 North East and Yorkshire     17
## 490  2020-06-02 North East and Yorkshire     23
## 491  2020-06-03 North East and Yorkshire     23
## 492  2020-06-04 North East and Yorkshire     17
## 493  2020-06-05 North East and Yorkshire     18
## 494  2020-06-06 North East and Yorkshire     21
## 495  2020-06-07 North East and Yorkshire     14
## 496  2020-06-08 North East and Yorkshire     11
## 497  2020-06-09 North East and Yorkshire     12
## 498  2020-06-10 North East and Yorkshire     19
## 499  2020-06-11 North East and Yorkshire      7
## 500  2020-06-12 North East and Yorkshire      9
## 501  2020-06-13 North East and Yorkshire     10
## 502  2020-06-14 North East and Yorkshire     11
## 503  2020-06-15 North East and Yorkshire      9
## 504  2020-06-16 North East and Yorkshire     10
## 505  2020-06-17 North East and Yorkshire      9
## 506  2020-06-18 North East and Yorkshire     11
## 507  2020-06-19 North East and Yorkshire      6
## 508  2020-06-20 North East and Yorkshire      4
## 509  2020-06-21 North East and Yorkshire      4
## 510  2020-06-22 North East and Yorkshire      6
## 511  2020-06-23 North East and Yorkshire      7
## 512  2020-06-24 North East and Yorkshire     10
## 513  2020-06-25 North East and Yorkshire      4
## 514  2020-06-26 North East and Yorkshire      7
## 515  2020-06-27 North East and Yorkshire      3
## 516  2020-06-28 North East and Yorkshire      5
## 517  2020-06-29 North East and Yorkshire      2
## 518  2020-06-30 North East and Yorkshire      4
## 519  2020-07-01 North East and Yorkshire      1
## 520  2020-07-02 North East and Yorkshire      4
## 521  2020-07-03 North East and Yorkshire      3
## 522  2020-07-04 North East and Yorkshire      4
## 523  2020-07-05 North East and Yorkshire      2
## 524  2020-07-06 North East and Yorkshire      2
## 525  2020-07-07 North East and Yorkshire      3
## 526  2020-07-08 North East and Yorkshire      3
## 527  2020-07-09 North East and Yorkshire      0
## 528  2020-07-10 North East and Yorkshire      0
## 529  2020-03-01               North West      0
## 530  2020-03-02               North West      0
## 531  2020-03-03               North West      0
## 532  2020-03-04               North West      0
## 533  2020-03-05               North West      1
## 534  2020-03-06               North West      0
## 535  2020-03-07               North West      0
## 536  2020-03-08               North West      1
## 537  2020-03-09               North West      0
## 538  2020-03-10               North West      0
## 539  2020-03-11               North West      0
## 540  2020-03-12               North West      2
## 541  2020-03-13               North West      3
## 542  2020-03-14               North West      1
## 543  2020-03-15               North West      4
## 544  2020-03-16               North West      2
## 545  2020-03-17               North West      4
## 546  2020-03-18               North West      6
## 547  2020-03-19               North West      7
## 548  2020-03-20               North West     10
## 549  2020-03-21               North West     11
## 550  2020-03-22               North West     13
## 551  2020-03-23               North West     15
## 552  2020-03-24               North West     21
## 553  2020-03-25               North West     21
## 554  2020-03-26               North West     29
## 555  2020-03-27               North West     36
## 556  2020-03-28               North West     28
## 557  2020-03-29               North West     46
## 558  2020-03-30               North West     67
## 559  2020-03-31               North West     52
## 560  2020-04-01               North West     86
## 561  2020-04-02               North West     96
## 562  2020-04-03               North West     95
## 563  2020-04-04               North West     98
## 564  2020-04-05               North West    102
## 565  2020-04-06               North West    100
## 566  2020-04-07               North West    135
## 567  2020-04-08               North West    127
## 568  2020-04-09               North West    119
## 569  2020-04-10               North West    117
## 570  2020-04-11               North West    138
## 571  2020-04-12               North West    125
## 572  2020-04-13               North West    129
## 573  2020-04-14               North West    131
## 574  2020-04-15               North West    114
## 575  2020-04-16               North West    135
## 576  2020-04-17               North West     98
## 577  2020-04-18               North West    113
## 578  2020-04-19               North West     71
## 579  2020-04-20               North West     83
## 580  2020-04-21               North West     76
## 581  2020-04-22               North West     86
## 582  2020-04-23               North West     85
## 583  2020-04-24               North West     66
## 584  2020-04-25               North West     66
## 585  2020-04-26               North West     55
## 586  2020-04-27               North West     54
## 587  2020-04-28               North West     57
## 588  2020-04-29               North West     63
## 589  2020-04-30               North West     59
## 590  2020-05-01               North West     45
## 591  2020-05-02               North West     56
## 592  2020-05-03               North West     55
## 593  2020-05-04               North West     48
## 594  2020-05-05               North West     48
## 595  2020-05-06               North West     44
## 596  2020-05-07               North West     49
## 597  2020-05-08               North West     42
## 598  2020-05-09               North West     30
## 599  2020-05-10               North West     42
## 600  2020-05-11               North West     35
## 601  2020-05-12               North West     38
## 602  2020-05-13               North West     25
## 603  2020-05-14               North West     26
## 604  2020-05-15               North West     33
## 605  2020-05-16               North West     32
## 606  2020-05-17               North West     24
## 607  2020-05-18               North West     31
## 608  2020-05-19               North West     35
## 609  2020-05-20               North West     27
## 610  2020-05-21               North West     27
## 611  2020-05-22               North West     26
## 612  2020-05-23               North West     31
## 613  2020-05-24               North West     26
## 614  2020-05-25               North West     31
## 615  2020-05-26               North West     27
## 616  2020-05-27               North West     27
## 617  2020-05-28               North West     28
## 618  2020-05-29               North West     20
## 619  2020-05-30               North West     19
## 620  2020-05-31               North West     13
## 621  2020-06-01               North West     12
## 622  2020-06-02               North West     27
## 623  2020-06-03               North West     22
## 624  2020-06-04               North West     22
## 625  2020-06-05               North West     16
## 626  2020-06-06               North West     26
## 627  2020-06-07               North West     20
## 628  2020-06-08               North West     23
## 629  2020-06-09               North West     17
## 630  2020-06-10               North West     16
## 631  2020-06-11               North West     16
## 632  2020-06-12               North West     11
## 633  2020-06-13               North West     10
## 634  2020-06-14               North West     15
## 635  2020-06-15               North West     16
## 636  2020-06-16               North West     15
## 637  2020-06-17               North West     13
## 638  2020-06-18               North West     13
## 639  2020-06-19               North West      7
## 640  2020-06-20               North West     11
## 641  2020-06-21               North West      7
## 642  2020-06-22               North West     11
## 643  2020-06-23               North West     13
## 644  2020-06-24               North West     13
## 645  2020-06-25               North West     15
## 646  2020-06-26               North West      6
## 647  2020-06-27               North West      7
## 648  2020-06-28               North West      9
## 649  2020-06-29               North West      7
## 650  2020-06-30               North West      6
## 651  2020-07-01               North West      2
## 652  2020-07-02               North West      6
## 653  2020-07-03               North West      6
## 654  2020-07-04               North West      4
## 655  2020-07-05               North West      5
## 656  2020-07-06               North West      9
## 657  2020-07-07               North West      6
## 658  2020-07-08               North West      3
## 659  2020-07-09               North West      9
## 660  2020-07-10               North West      0
## 661  2020-03-01               South East      0
## 662  2020-03-02               South East      0
## 663  2020-03-03               South East      1
## 664  2020-03-04               South East      0
## 665  2020-03-05               South East      1
## 666  2020-03-06               South East      0
## 667  2020-03-07               South East      0
## 668  2020-03-08               South East      1
## 669  2020-03-09               South East      1
## 670  2020-03-10               South East      1
## 671  2020-03-11               South East      1
## 672  2020-03-12               South East      0
## 673  2020-03-13               South East      1
## 674  2020-03-14               South East      1
## 675  2020-03-15               South East      5
## 676  2020-03-16               South East      8
## 677  2020-03-17               South East      7
## 678  2020-03-18               South East     10
## 679  2020-03-19               South East      9
## 680  2020-03-20               South East     13
## 681  2020-03-21               South East      7
## 682  2020-03-22               South East     25
## 683  2020-03-23               South East     20
## 684  2020-03-24               South East     22
## 685  2020-03-25               South East     29
## 686  2020-03-26               South East     35
## 687  2020-03-27               South East     34
## 688  2020-03-28               South East     36
## 689  2020-03-29               South East     55
## 690  2020-03-30               South East     58
## 691  2020-03-31               South East     65
## 692  2020-04-01               South East     66
## 693  2020-04-02               South East     55
## 694  2020-04-03               South East     72
## 695  2020-04-04               South East     80
## 696  2020-04-05               South East     82
## 697  2020-04-06               South East     88
## 698  2020-04-07               South East    100
## 699  2020-04-08               South East     83
## 700  2020-04-09               South East    104
## 701  2020-04-10               South East     88
## 702  2020-04-11               South East     88
## 703  2020-04-12               South East     88
## 704  2020-04-13               South East     84
## 705  2020-04-14               South East     65
## 706  2020-04-15               South East     72
## 707  2020-04-16               South East     56
## 708  2020-04-17               South East     86
## 709  2020-04-18               South East     57
## 710  2020-04-19               South East     70
## 711  2020-04-20               South East     87
## 712  2020-04-21               South East     51
## 713  2020-04-22               South East     54
## 714  2020-04-23               South East     57
## 715  2020-04-24               South East     64
## 716  2020-04-25               South East     51
## 717  2020-04-26               South East     51
## 718  2020-04-27               South East     40
## 719  2020-04-28               South East     40
## 720  2020-04-29               South East     47
## 721  2020-04-30               South East     29
## 722  2020-05-01               South East     37
## 723  2020-05-02               South East     36
## 724  2020-05-03               South East     17
## 725  2020-05-04               South East     35
## 726  2020-05-05               South East     29
## 727  2020-05-06               South East     25
## 728  2020-05-07               South East     27
## 729  2020-05-08               South East     26
## 730  2020-05-09               South East     28
## 731  2020-05-10               South East     19
## 732  2020-05-11               South East     25
## 733  2020-05-12               South East     27
## 734  2020-05-13               South East     18
## 735  2020-05-14               South East     32
## 736  2020-05-15               South East     25
## 737  2020-05-16               South East     22
## 738  2020-05-17               South East     18
## 739  2020-05-18               South East     22
## 740  2020-05-19               South East     12
## 741  2020-05-20               South East     22
## 742  2020-05-21               South East     15
## 743  2020-05-22               South East     17
## 744  2020-05-23               South East     21
## 745  2020-05-24               South East     17
## 746  2020-05-25               South East     13
## 747  2020-05-26               South East     19
## 748  2020-05-27               South East     18
## 749  2020-05-28               South East     12
## 750  2020-05-29               South East     21
## 751  2020-05-30               South East      8
## 752  2020-05-31               South East     12
## 753  2020-06-01               South East     11
## 754  2020-06-02               South East     13
## 755  2020-06-03               South East     18
## 756  2020-06-04               South East     11
## 757  2020-06-05               South East     11
## 758  2020-06-06               South East     10
## 759  2020-06-07               South East     12
## 760  2020-06-08               South East      8
## 761  2020-06-09               South East     10
## 762  2020-06-10               South East     11
## 763  2020-06-11               South East      5
## 764  2020-06-12               South East      6
## 765  2020-06-13               South East      6
## 766  2020-06-14               South East      7
## 767  2020-06-15               South East      8
## 768  2020-06-16               South East     13
## 769  2020-06-17               South East      9
## 770  2020-06-18               South East      4
## 771  2020-06-19               South East      7
## 772  2020-06-20               South East      5
## 773  2020-06-21               South East      3
## 774  2020-06-22               South East      2
## 775  2020-06-23               South East      8
## 776  2020-06-24               South East      7
## 777  2020-06-25               South East      5
## 778  2020-06-26               South East      8
## 779  2020-06-27               South East      8
## 780  2020-06-28               South East      6
## 781  2020-06-29               South East      5
## 782  2020-06-30               South East      5
## 783  2020-07-01               South East      2
## 784  2020-07-02               South East      7
## 785  2020-07-03               South East      3
## 786  2020-07-04               South East      5
## 787  2020-07-05               South East      4
## 788  2020-07-06               South East      3
## 789  2020-07-07               South East      5
## 790  2020-07-08               South East      2
## 791  2020-07-09               South East      4
## 792  2020-07-10               South East      0
## 793  2020-03-01               South West      0
## 794  2020-03-02               South West      0
## 795  2020-03-03               South West      0
## 796  2020-03-04               South West      0
## 797  2020-03-05               South West      0
## 798  2020-03-06               South West      0
## 799  2020-03-07               South West      0
## 800  2020-03-08               South West      0
## 801  2020-03-09               South West      0
## 802  2020-03-10               South West      0
## 803  2020-03-11               South West      1
## 804  2020-03-12               South West      0
## 805  2020-03-13               South West      0
## 806  2020-03-14               South West      1
## 807  2020-03-15               South West      0
## 808  2020-03-16               South West      0
## 809  2020-03-17               South West      2
## 810  2020-03-18               South West      2
## 811  2020-03-19               South West      4
## 812  2020-03-20               South West      3
## 813  2020-03-21               South West      6
## 814  2020-03-22               South West      7
## 815  2020-03-23               South West      8
## 816  2020-03-24               South West      7
## 817  2020-03-25               South West      9
## 818  2020-03-26               South West     11
## 819  2020-03-27               South West     13
## 820  2020-03-28               South West     21
## 821  2020-03-29               South West     18
## 822  2020-03-30               South West     23
## 823  2020-03-31               South West     23
## 824  2020-04-01               South West     21
## 825  2020-04-02               South West     23
## 826  2020-04-03               South West     30
## 827  2020-04-04               South West     42
## 828  2020-04-05               South West     32
## 829  2020-04-06               South West     34
## 830  2020-04-07               South West     39
## 831  2020-04-08               South West     47
## 832  2020-04-09               South West     24
## 833  2020-04-10               South West     46
## 834  2020-04-11               South West     43
## 835  2020-04-12               South West     23
## 836  2020-04-13               South West     27
## 837  2020-04-14               South West     24
## 838  2020-04-15               South West     32
## 839  2020-04-16               South West     29
## 840  2020-04-17               South West     33
## 841  2020-04-18               South West     25
## 842  2020-04-19               South West     31
## 843  2020-04-20               South West     26
## 844  2020-04-21               South West     26
## 845  2020-04-22               South West     23
## 846  2020-04-23               South West     17
## 847  2020-04-24               South West     19
## 848  2020-04-25               South West     15
## 849  2020-04-26               South West     27
## 850  2020-04-27               South West     13
## 851  2020-04-28               South West     17
## 852  2020-04-29               South West     15
## 853  2020-04-30               South West     26
## 854  2020-05-01               South West      6
## 855  2020-05-02               South West      7
## 856  2020-05-03               South West     10
## 857  2020-05-04               South West     17
## 858  2020-05-05               South West     14
## 859  2020-05-06               South West     19
## 860  2020-05-07               South West     16
## 861  2020-05-08               South West      6
## 862  2020-05-09               South West     11
## 863  2020-05-10               South West      5
## 864  2020-05-11               South West      8
## 865  2020-05-12               South West      7
## 866  2020-05-13               South West      7
## 867  2020-05-14               South West      6
## 868  2020-05-15               South West      4
## 869  2020-05-16               South West      4
## 870  2020-05-17               South West      6
## 871  2020-05-18               South West      4
## 872  2020-05-19               South West      6
## 873  2020-05-20               South West      1
## 874  2020-05-21               South West      9
## 875  2020-05-22               South West      6
## 876  2020-05-23               South West      6
## 877  2020-05-24               South West      3
## 878  2020-05-25               South West      8
## 879  2020-05-26               South West     11
## 880  2020-05-27               South West      5
## 881  2020-05-28               South West     10
## 882  2020-05-29               South West      7
## 883  2020-05-30               South West      3
## 884  2020-05-31               South West      2
## 885  2020-06-01               South West      7
## 886  2020-06-02               South West      2
## 887  2020-06-03               South West      7
## 888  2020-06-04               South West      2
## 889  2020-06-05               South West      2
## 890  2020-06-06               South West      1
## 891  2020-06-07               South West      3
## 892  2020-06-08               South West      3
## 893  2020-06-09               South West      0
## 894  2020-06-10               South West      1
## 895  2020-06-11               South West      2
## 896  2020-06-12               South West      2
## 897  2020-06-13               South West      2
## 898  2020-06-14               South West      0
## 899  2020-06-15               South West      1
## 900  2020-06-16               South West      2
## 901  2020-06-17               South West      0
## 902  2020-06-18               South West      0
## 903  2020-06-19               South West      0
## 904  2020-06-20               South West      2
## 905  2020-06-21               South West      0
## 906  2020-06-22               South West      1
## 907  2020-06-23               South West      1
## 908  2020-06-24               South West      1
## 909  2020-06-25               South West      0
## 910  2020-06-26               South West      3
## 911  2020-06-27               South West      0
## 912  2020-06-28               South West      0
## 913  2020-06-29               South West      1
## 914  2020-06-30               South West      0
## 915  2020-07-01               South West      0
## 916  2020-07-02               South West      0
## 917  2020-07-03               South West      0
## 918  2020-07-04               South West      0
## 919  2020-07-05               South West      1
## 920  2020-07-06               South West      0
## 921  2020-07-07               South West      0
## 922  2020-07-08               South West      2
## 923  2020-07-09               South West      0
## 924  2020-07-10               South West      0

1.5 Completion date

We extract the completion date from the NHS Pathways file timestamp:


database_date <- attr(x, "timestamp")
database_date
## [1] "2020-07-09"

The completion date of the NHS Pathways data is Thursday 09 Jul 2020.

1.6 Auxiliary functions

These are functions which will be used further in the analyses.

Function to estimate the generalised R-squared as the proportion of deviance explained by a given model:


## Function to calculate R2 for Poisson model
## not adjusted for model complexity but all models have the same DF here

Rsq <- function(x) {
  1 - (x$deviance / x$null.deviance)
}

Function to extract growth rates per region as well as halving times, and the associated 95% confidence intervals:


## function to extract the coefficients, find the level of the intercept,
## reconstruct the values of r, get confidence intervals

get_r <- function(model) {
  ##  extract coefficients and conf int
  out <- data.frame(r = coef(model))  %>%
    rownames_to_column("var") %>% 
    cbind(confint(model)) %>%
    filter(!grepl("day_of_week", var)) %>% 
    filter(grepl("day", var)) %>%
    rename(lower_95 = "2.5 %",
           upper_95 = "97.5 %") %>%
    mutate(var = sub("day:", "", var))
  
  ## reconstruct values: intercept + region-coefficient
  for (i in 2:nrow(out)) {
    out[i, -1] <- out[1, -1] + out[i, -1]
  }
  
  ## find the name of the intercept, restore regions names
  out <- out %>%
    mutate(nhs_region = model$xlevels$nhs_region) %>%
    select(nhs_region, everything(), -var)
  
  ## find halving times
  halving <- log(0.5) / out[,-1] %>%
    rename(halving_t = r,
           halving_t_lower_95 = lower_95,
           halving_t_upper_95 = upper_95)
  
  ## set halving times with exclusion intervals to NA
  no_halving <- out$lower_95 < 0 & out$upper_95 > 0
  halving[no_halving, ] <- NA_real_
  
  ## return all data
  cbind(out, halving)
  
}

Functions used in the correlation analysis between NHS Pathways reports and deaths:

## Function to calculate Pearson's correlation between deaths and lagged
## reports. Note that `pearson` can be replaced with `spearman` for rank
## correlation.

getcor <- function(x, ndx) {
  return(cor(x$deaths[ndx],
             x$note_lag[ndx],
             use = "complete.obs",
             method = "pearson"))
}

## Catch if sample size throws an error
getcor2 <- possibly(getcor, otherwise = NA)

getboot <- function(x) {
  result <- boot::boot.ci(boot::boot(x, getcor2, R = 1000), 
                           type = "bca")
  return(data.frame(n = sum(!is.na(x$note_lag) & !is.na(x$deaths)),
                    r = result$t0,
                    r_low = result$bca[4],
                    r_hi = result$bca[5]))
}

Function to classify the day of the week into weekend, Monday, and the rest:


## Fn to add day of week
day_of_week <- function(df) {
  df %>% 
    dplyr::mutate(day_of_week = lubridate::wday(date, label = TRUE)) %>% 
    dplyr::mutate(day_of_week = dplyr::case_when(
      day_of_week %in% c("Sat", "Sun") ~ "weekend",
      day_of_week %in% c("Mon") ~ "monday",
      !(day_of_week %in% c("Sat", "Sun", "Mon")) ~ "rest_of_week"
    ) %>% 
      factor(levels = c("rest_of_week", "monday", "weekend")))
}

Custom color palettes, color scales, and vectors of colors:


pal <- c("#006212",
         "#ae3cab",
         "#00db90",
         "#960c00",
         "#55aaff",
         "#ff7e78",
         "#00388d")

age.pal <- viridis::viridis(3,begin = 0.1, end = 0.7)

3 Comparison with deaths time series

3.1 Outline

We want to explore the correlation between NHS Pathways reports and deaths, and assess the potential for reports to be used as an early warning system for disease resurgence.

Death data are publically available. We truncate the time series to avoid bias from reporting delay - we assume a conservative delay of three weeks.

3.2 Lagged correlation

We calculate Pearson’s correlation coefficient between deaths and NHS Pathways notifications using different lags. Confidence intervals are obtained using bootstrap. Note that results were also confirmed using Spearman’s rank correlation.

First we join the NHS Pathways and death data, and aggregate over all England:

## truncate death data for reporting delay
trunc_date <- max(dth$date_report) - delay_max

dth_trunc <- dth %>%
  rename(date = date_report) %>%
  filter(date <= trunc_date) 

## join with notification data
all_data <- x %>% 
  filter(!is.na(nhs_region)) %>%
  group_by(date, nhs_region) %>%
  summarise(count = sum(count, na.rm = T)) %>%
  ungroup %>%
  inner_join(dth_trunc,
             by = c("date","nhs_region"))

all_tot <- all_data %>%
  group_by(date) %>%
  summarise(count = sum(count, na.rm = TRUE),
            deaths = sum(deaths, na.rm = TRUE)) 

We calculate correlation with lagged NHS Pathways reports from 0 to 30 days behind deaths:


## Calculate all correlations + bootstrap CIs
lag_cor <- data.frame()
for (i in 0:30) {
  
  ## lag reports
  summary <- all_tot %>% 
    mutate(note_lag = lag(count, i)) %>%
    ## calculate rank correlation and bootstrap CI
    getboot(.) %>%
    mutate(lag = i)

  lag_cor <- bind_rows(lag_cor, summary)
}

cor_vs_lag <- ggplot(lag_cor, aes(lag, r)) +
  theme_bw() +
  geom_ribbon(aes(ymin = r_low, ymax = r_hi), alpha = 0.2) +
  geom_hline(yintercept = 0, lty = "longdash") +
  geom_point() +
  geom_line() +
  labs(x = "Lag between NHS pathways and death data (days)",
       y = "Pearson's correlation") +
  large_txt
cor_vs_lag


l_opt <- which.max(lag_cor$r)

This analysis suggests that the best lag is 23 days. We then compare and plot the number of deaths reported against the number of NHS Pathways reports lagged by 23 days.


all_tot <- all_tot %>%
  rename(date_death = date) %>%
  mutate(note_lag = lag(count, lag_cor$lag[l_opt]),
         note_lag_c = (note_lag - mean(note_lag, na.rm = T)),
         date_note = lag(date_death,16))

lag_mod <- glm(deaths ~ note_lag, data = all_tot, family = "quasipoisson")

summary(lag_mod)
## 
## Call:
## glm(formula = deaths ~ note_lag, family = "quasipoisson", data = all_tot)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -12.534   -4.050   -0.120    3.361    7.653  
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 4.661e+00  6.267e-02   74.38   <2e-16 ***
## note_lag    1.399e-05  6.494e-07   21.54   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for quasipoisson family taken to be 21.47912)
## 
##     Null deviance: 10788.4  on 70  degrees of freedom
## Residual deviance:  1570.1  on 69  degrees of freedom
##   (23 observations deleted due to missingness)
## AIC: NA
## 
## Number of Fisher Scoring iterations: 4

exp(coefficients(lag_mod))
## (Intercept)    note_lag 
##  105.738094    1.000014
exp(confint(lag_mod))
##                 2.5 %     97.5 %
## (Intercept) 93.345860 119.344263
## note_lag     1.000013   1.000015

Rsq(lag_mod)
## [1] 0.8544628

mod_fit <- as.data.frame(predict(lag_mod, type = "link", se.fit = TRUE)[1:2])

all_tot_pred <- 
  all_tot %>%
  filter(!is.na(note_lag)) %>%
  mutate(pred = mod_fit$fit,
         pred.se = mod_fit$se.fit,
         low = exp(pred - 1.96*pred.se),
         hi = exp(pred + 1.96*pred.se))


glm_fit <- all_tot_pred %>% 
    filter(!is.na(note_lag)) %>%
  ggplot(aes(x = note_lag, y = deaths)) +
  geom_point() + 
  geom_line(aes(y = exp(pred))) + 
  geom_ribbon(aes(ymin = low, ymax = hi), alpha = 0.3, col = "grey") +
  theme_bw() +
  labs(y = "Daily number of\ndeaths reported",
       x = "Daily number of NHS Pathways reports") +
  large_txt

glm_fit

4 Supplementary figures

4.1 Serial interval distribution

This is a comparison of gamma versus lognormal distribution for the serial interval used to convert r to R in our analysis. Both distributions are parameterised with mean 4.7 and standard deviation 2.9.

SI_param <- epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale, w = 0.5)

SI_distribution2 <- distcrete::distcrete("lnorm", interval = 1,
                                        meanlog = log(4.7),
                                        sdlog = log(2.9), w = 0.5)

SI_dist1 <- data.frame(x = SI_distribution$r(1e5)) 
SI_dist1 <- count(SI_dist1, x) %>%
    ggplot() +
    geom_col(aes(x = x, y = n)) +
    labs(x = "Serial interval (days)", y = "Frequency") +
    scale_x_continuous(breaks = seq(0, 30, 5)) +
    theme_bw()

SI_dist2 <- data.frame(x = SI_distribution2$r(1e5)) 
SI_dist2 <- count(SI_dist2, x) %>%
    ggplot() +
    geom_col(aes(x = x, y = n)) +
    labs(x = "Serial interval (days)", y = "Frequency") +
    scale_x_continuous(breaks = seq(0, 200, 20), limits = c(0, 200)) +
    theme_bw()


ggpubr::ggarrange(SI_dist1,
                  SI_dist2,
                  nrow = 1,
                  labels = "AUTO") 

4.2 Sensitivity analysis - 7 or 21 days moving window

We reproduce the window analysis with either a 7 or 21 days window for sensitivity purposes.

First with the 7 days window:

## set moving time window (1/2/3 weeks)
w <- 7

# create empty df
r_all_sliding_7days <- NULL

## make data for model
x_model_all_moving <- x %>%
  filter(!is.na(nhs_region)) %>% 
  group_by(date, nhs_region) %>%
  summarise(n = sum(count)) 

unique_dates <- unique(x_model_all_moving$date)

for (i in 1:(length(unique_dates) - w)) {
  
  date_i <- unique_dates[i]
  
  date_i_max <- date_i + w
  
  model_data <- x_model_all_moving %>%
    filter(date >= date_i & date < date_i_max) %>%
    mutate(day = as.integer(date - date_i)) %>% 
    day_of_week()
  
  
  mod <- glm(n ~ day * nhs_region + day_of_week,
             data = model_data,
             family = 'quasipoisson')
  
  # get growth rate
  r <- get_r(mod)
  r$w_min <- date_i
  r$w_max <- date_i_max
  
  # combine all estimates
  r_all_sliding_7days <- bind_rows(r_all_sliding_7days, r)
  
}

#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale,
                                        w = 0.5)

#convert growth rates r to R0
r_all_sliding_7days <- r_all_sliding_7days %>%
  mutate(R = epitrix::r2R0(r, SI_distribution),
         R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
         R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))
# plot
plot_growth <-
  r_all_sliding_7days %>%
  ggplot(aes(x = w_max, y = r)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated daily growth rate (r)") +
  scale_colour_manual(values = pal)
plot_R <- r_all_sliding_7days %>%
  ggplot(aes(x = w_max, y = R)) +
  geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 1, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated effective reproduction\nnumber (Re)") +
  scale_colour_manual(values = pal)

R <- r_all_sliding_7days %>%
  mutate(lower_95 = R_lower_95, 
         upper_95 = R_upper_95,
         value = R,
         measure = "R",
         reference = 1)

r_R <- r_all_sliding_7days %>%
  mutate(measure = "r",
         value = r,
         reference = 0) %>%
  bind_rows(R)

r_R_7 <- r_R %>%
  ggplot(aes(x = w_max, y = value)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(aes(yintercept = reference), linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0,0, "cm"),
        strip.background = element_blank(),
        strip.placement = "outside"
  ) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "", y = "") +
  scale_colour_manual(values = pal) +
  facet_grid(rows = vars(measure),
             scales = "free_y",
             switch = "y",
             labeller = as_labeller(c(r = "Daily growth rate (r)",
                                      R = "Effective reproduction\nnumber (Re)")))

Then with the 21 days window:

## set moving time window (1/2/3 weeks)
w <- 21

# create empty df
r_all_sliding_21days <- NULL

## make data for model
x_model_all_moving <- x %>%
  filter(!is.na(nhs_region)) %>% 
  group_by(date, nhs_region) %>%
  summarise(n = sum(count)) 

unique_dates <- unique(x_model_all_moving$date)

for (i in 1:(length(unique_dates) - w)) {
  
  date_i <- unique_dates[i]
  
  date_i_max <- date_i + w
  
  model_data <- x_model_all_moving %>%
    filter(date >= date_i & date < date_i_max) %>%
    mutate(day = as.integer(date - date_i)) %>% 
    day_of_week()
  
  
  mod <- glm(n ~ day * nhs_region + day_of_week,
             data = model_data,
             family = 'quasipoisson')
  
  # get growth rate
  r <- get_r(mod)
  r$w_min <- date_i
  r$w_max <- date_i_max
  
  # combine all estimates
  r_all_sliding_21days <- bind_rows(r_all_sliding_21days, r)
  
}

#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale,
                                        w = 0.5)

#convert growth rates r to R0
r_all_sliding_21days <- r_all_sliding_21days %>%
  mutate(R = epitrix::r2R0(r, SI_distribution),
         R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
         R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))
# plot
plot_growth <-
  r_all_sliding_21days %>%
  ggplot(aes(x = w_max, y = r)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated daily growth rate (r)") +
  scale_colour_manual(values = pal)
# plot
plot_R <-
  r_all_sliding_21days %>%
  ggplot(aes(x = w_max, y = R)) +
  geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 1, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated effective reproduction\nnumber (Re)") +
  scale_colour_manual(values = pal)

R <- r_all_sliding_21days %>%
  mutate(lower_95 = R_lower_95, 
         upper_95 = R_upper_95,
         value = R,
         measure = "R",
         reference = 1)

r_R <- r_all_sliding_21days %>%
  mutate(measure = "r",
         value = r,
         reference = 0) %>%
  bind_rows(R)

r_R_21 <- r_R %>%
  ggplot(aes(x = w_max, y = value)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(aes(yintercept = reference), linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0,0, "cm"),
        strip.background = element_blank(),
        strip.placement = "outside"
  ) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "", y = "") +
  scale_colour_manual(values = pal) +
  facet_grid(rows = vars(measure),
             scales = "free_y",
             switch = "y",
             labeller = as_labeller(c(r = "Daily growth rate (r)",
                                      R = "Effective reproduction\nnumber (Re)")))

And we combine both outputs into a single plot:


ggpubr::ggarrange(r_R_7,
                  r_R_21,
                  nrow = 2,
                  labels = "AUTO",
                  common.legend = TRUE,
                  legend = "bottom") 

4.3 Correlation between NHS Pathways reports and deaths by NHS region


lag_cor_reg <- data.frame()

for (i in 0:30) {

  summary <-
    all_data %>%
    group_by(nhs_region) %>%
    mutate(note_lag = lag(count, i)) %>%
    ## calculate rank correlation and bootstrap CI for each region
    group_modify(~getboot(.x)) %>%
    mutate(lag = i)
  
  lag_cor_reg <- bind_rows(lag_cor_reg, summary)
}

cor_vs_lag_reg <- 
lag_cor_reg %>%
ggplot(aes(lag, r, col = nhs_region)) +
  geom_hline(yintercept = 0, lty = "longdash") +
  geom_ribbon(aes(ymin = r_low, ymax = r_hi, col = NULL, fill = nhs_region), alpha = 0.2) +
  geom_point() +
  geom_line() +
  facet_wrap(~nhs_region) +
  scale_color_manual(values = pal) +
  scale_fill_manual(values = pal, guide = F) +  
  theme_bw() +
  labs(x = "Lag between NHS pathways and death data (days)", y = "Pearson's correlation", col = "NHS region") +
  theme(legend.position = "bottom") +
  guides(color = guide_legend(override.aes = list(fill = NA)))

cor_vs_lag_reg

5 Export data

We save the tables created during our analysis:


if (!dir.exists("excel_tables")) {
  dir.create("excel_tables")
}


## list all tables, and loop over export
tables_to_export <- c("r_all_sliding", "lag_cor")

for (e in tables_to_export) {
  rio::export(get(e),
              file.path("excel_tables",
                        paste0(e, ".xlsx")))
}

## also export result from regression on lagged data 
rio::export(lag_mod, file.path("excel_tables", "lag_mod.rds"))

6 System information

6.1 Outline

The following information documents the system on which the document was compiled.

6.2 System

This provides information on the operating system.

Sys.info()
##                                                                                            sysname 
##                                                                                           "Darwin" 
##                                                                                            release 
##                                                                                           "19.5.0" 
##                                                                                            version 
## "Darwin Kernel Version 19.5.0: Tue May 26 20:41:44 PDT 2020; root:xnu-6153.121.2~2/RELEASE_X86_64" 
##                                                                                           nodename 
##                                                                                   "Mac-1666.local" 
##                                                                                            machine 
##                                                                                           "x86_64" 
##                                                                                              login 
##                                                                                             "root" 
##                                                                                               user 
##                                                                                           "runner" 
##                                                                                     effective_user 
##                                                                                           "runner"

6.3 R environment

This provides information on the version of R used:

R.version
##                _                           
## platform       x86_64-apple-darwin17.0     
## arch           x86_64                      
## os             darwin17.0                  
## system         x86_64, darwin17.0          
## status                                     
## major          4                           
## minor          0.2                         
## year           2020                        
## month          06                          
## day            22                          
## svn rev        78730                       
## language       R                           
## version.string R version 4.0.2 (2020-06-22)
## nickname       Taking Off Again

6.4 R packages

This provides information on the packages used:

sessionInfo()
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.5
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] ggnewscale_0.4.1     ggpubr_0.4.0         lubridate_1.7.9     
##  [4] chngpt_2020.5-21     cyphr_1.1.0          DT_0.14             
##  [7] kableExtra_1.1.0     janitor_2.0.1        remotes_2.1.1       
## [10] projections_0.5.1    earlyR_0.0.1         epitrix_0.2.2       
## [13] distcrete_1.0.3      incidence_1.7.1      rio_0.5.16          
## [16] reshape2_1.4.4       rvest_0.3.5          xml2_1.3.2          
## [19] linelist_0.0.40.9000 forcats_0.5.0        stringr_1.4.0       
## [22] dplyr_1.0.0          purrr_0.3.4          readr_1.3.1         
## [25] tidyr_1.1.0          tibble_3.0.3         ggplot2_3.3.2       
## [28] tidyverse_1.3.0      here_0.1             reportfactory_0.0.5 
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-148      fs_1.4.2          webshot_0.5.2     httr_1.4.1       
##  [5] rprojroot_1.3-2   tools_4.0.2       backports_1.1.8   utf8_1.1.4       
##  [9] R6_2.4.1          mgcv_1.8-31       DBI_1.1.0         colorspace_1.4-1 
## [13] withr_2.2.0       gridExtra_2.3     tidyselect_1.1.0  sodium_1.1       
## [17] curl_4.3          compiler_4.0.2    cli_2.0.2         labeling_0.3     
## [21] matchmaker_0.1.1  scales_1.1.1      digest_0.6.25     foreign_0.8-80   
## [25] rmarkdown_2.3     pkgconfig_2.0.3   htmltools_0.5.0   dbplyr_1.4.4     
## [29] htmlwidgets_1.5.1 rlang_0.4.7       readxl_1.3.1      rstudioapi_0.11  
## [33] farver_2.0.3      generics_0.0.2    jsonlite_1.7.0    crosstalk_1.1.0.1
## [37] car_3.0-8         zip_2.0.4         magrittr_1.5      kyotil_2019.11-22
## [41] Matrix_1.2-18     Rcpp_1.0.5        munsell_0.5.0     fansi_0.4.1      
## [45] viridis_0.5.1     abind_1.4-5       lifecycle_0.2.0   stringi_1.4.6    
## [49] yaml_2.2.1        carData_3.0-4     snakecase_0.11.0  MASS_7.3-51.6    
## [53] plyr_1.8.6        grid_4.0.2        blob_1.2.1        crayon_1.3.4     
## [57] lattice_0.20-41   cowplot_1.0.0     splines_4.0.2     haven_2.3.1      
## [61] hms_0.5.3         knitr_1.29        pillar_1.4.6      boot_1.3-25      
## [65] ggsignif_0.6.0    reprex_0.3.0      glue_1.4.1        evaluate_0.14    
## [69] data.table_1.12.8 modelr_0.1.8      vctrs_0.3.1       selectr_0.4-2    
## [73] cellranger_1.1.0  gtable_0.3.0      assertthat_0.2.1  xfun_0.15        
## [77] openxlsx_4.1.5    broom_0.7.0       rstatix_0.6.0     survival_3.1-12  
## [81] viridisLite_0.3.0 ellipsis_0.3.1